Structural basis for specific activation of the Rab11 GTPase by the TRAPPII complex

Secretion is an essential cellular function in which proteins and lipids are transported from the Golgi to the plasma membrane via secretory vesicles. The formation of secretory vesicles is regulated by activation of the Rab GTPase Rab11. The activation of Rab GTPases at membrane compartments is dependent on the localization of their specific Guanosine Exchange Factors (GEFs), which catalyze the exchange of GDP with GTP and stabilize the active GTPase on the membrane. The multisubunit TRAPPII complex acts as Rab11 GEF and recruits it to the trans-Golgi network (TGN) membrane. More than 60 different Rabs are present in mammals and budding yeast has 11 different Rabs. Specific localization of each of these Rabs to different membrane compartments is important for determination of organelle identity and membrane organization of these compartments. While multiple GTPases and GEFs localize at the TGN, the mechanistic details of how TRAPPII specifically activates Rab11, and not other GTPases, is unknown. Moreover, another related GEF, the TRAPPIII complex, shares the same catalytic subunits with TRAPPII and yet activates another GTPase, Rab1. A steric gating mechanism has been proposed in which TRAPPII selects against Rab1 based on the length of the C-terminal hypervariable domain. We determined the structure of yeast TRAPPII bound to its substrate Rab11 using cryo-EM at an overall resolution of 3.7Å. Analysis of the atomic structure has revealed specific interactions between Rab11 and the TRAPPII complex, and how TRAPPII interacts with the membrane surface. We tested the physiological relevance of these observed interactions using in vivo functional studies and in vitro reconstitution of nucleotide exchange. We show that the TRAPPII subunit Trs130 provides a 'leg' which lifts the TRAPP catalytic site above the membrane, thereby preventing access to the catalytic site by Rab1. TRAPPIII complex selects against Rab11 based on repulsive interactions with the catalytic subunits. We also show an alternative conformation of the TRAPPII complex which may facilitate access of Rab11 to the TRAPP catalytic site. Taken together, these experiments reveal the mechanism of specific activation of Rab11 on the membrane by TRAPPII, a key step for initiation of secretory vesicle formation. As Rab11 and the TRAPPII complex are conserved throughout eukaryotes, this mechanism may be widely conserved across all eukaryotic secretory systems.